Just guessing here from what I've seen in Croatia, but I'd say it is less a problem with Israel as such, and more with how certain prominent advocates of "nationalism is Nazism" are Jews, and - perhaps more importantly - always use Jewish casualties in World War II to support their position. In Croatia, we have Ivo and Slavko Goldstein, who not only accuse anyone who attacks Communism as being Nazis, but also deny the existence of post-war camp in Jasenovac (concentration camp there was active until late 1947. / early 1948.). And the fact that they always play the "Holocaust" and "Jewish victim" cards means that Jews as such get a bad rep, simply by proxy.
Honestly, such prominent "antifascist" "crusaders" are likely the worst thing for Jews, PR-wise, despite the fact that they actually have no connection to what Jews as such think. Kinda like how most of the Left hates white people for colonialism, despite the fact that most of the white countries were victims of colonialism (such as the entirety of Central Europe and Balkans).